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8b6ddb1 Merge pull request common-workflow-language#461 from MarkRobbo/rdfs-namespace
eb64c56 Add rdfs namespaces where used
e5f4086 Merge pull request common-workflow-language#416 from common-workflow-language/mr-c-patch-1
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15a7d51 Merge pull request common-workflow-language#452 from common-workflow-language/hmenager-patch-1
78940a8 Add ELIXIR + BioExcel participating organizations
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506508b Merge pull request common-workflow-language#432 from michael-kotliar/master
dfbb124 update list of schedulers and platforms for Toil
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e150035 Merge pull request common-workflow-language#426 from common-workflow-language/fix-wc-test
6acb016 Fix wc test by using wc -l to avoid padding issues on different implementions of 'wc' (!)
d80919e Revert "Fix identifier conflicts (checked by cwltool for the first time) by giving ids"
f2ea521 Merge pull request common-workflow-language#418 from mdmiller53/master
2ade169 Update README.md
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fcc593a Fix identifier conflicts (checked by cwltool for the first time) by giving ids to embedded tools and workflows.
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f6b6f74 Merge pull request common-workflow-language#409 from common-workflow-language/LourensVeen-uml-sketch
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e6dc6e4 Use ShellCommandRequirement for stderr tests.
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f0f8b67 Sync v1.1 conformance test suite to changes in v1.0 suite.
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1d5c5b9 document Toil's slurm support
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Common Workflow Language
========================

[![GitHub stars](https://img.shields.io/github/stars/common-workflow-language/common-workflow-language.svg)](https://github.com/common-workflow-language/common-workflow-language/stargazers) [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[![GitHub stars](https://img.shields.io/github/stars/common-workflow-language/common-workflow-language.svg)](https://github.com/common-workflow-language/common-workflow-language/stargazers) [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [**Support**](#Support)

The Common Workflow Language (CWL) is a specification for describing analysis
workflows and tools that are portable and scalable across a variety of software
and hardware environments, from workstations to cluster, cloud, and high
performance computing (HPC) environments. CWL is designed to meet the needs of
data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy,
Physics, and Chemistry.
workflows and tools in a way that makes them portable and scalable across a
variety of software and hardware environments, from workstations to cluster,
cloud, and high performance computing (HPC) environments. CWL is designed to
meet the needs of data-intensive science, such as Bioinformatics, Medical
Imaging, Astronomy, Physics, and Chemistry.

CWL is developed by an informal, multi-vendor working group consisting of
organizations and individuals interested enabling scientists to share data
analysis workflows. [The CWL project is on Github.](https://github.com/common-workflow-language/common-workflow-language)
organizations and individuals aiming to enable scientists to share data
analysis workflows. [The CWL project is on Github](https://github.com/common-workflow-language/common-workflow-language) and we follow the [Open-Stand.org principles for collaborative open standards development](https://open-stand.org/about-us/principles/)

[![Open Stand badge](http://standards.ieee.org/images/openstand/128x128-blue2.png)](https://open-stand.org/about-us/principles/).

CWL builds on technologies such as [JSON-LD](http://json-ld.org)
for data modeling and [Docker](http://docker.com) for portable runtime
Expand Down Expand Up @@ -40,17 +42,19 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2

## Implementations

|Software|Description|CWL support|Platform support|Platform Maturity|
|--------|-----------|-----------|--------|--------|
|[cwltool](https://github.com/common-workflow-language/cwltool)|Reference implementation of CWL|[![Build Status](https://ci.commonwl.org/job/cwltool-conformance/badge/icon)](http://ci.commonwl.org/job/cwltool-conformance/lastBuild/testReport/)|Linux, OS X, local execution only|Production|
|[Arvados](https://arvados.org)|Distributed computing platform for data analysis on massive data sets. [Using CWL on Arvados](http://doc.arvados.org/user/cwl/cwl-runner.html)|[![Build Status](https://ci.commonwl.org/job/arvados-conformance/badge/icon)](http://ci.commonwl.org/job/arvados-conformance/lastBuild/testReport/)|AWS, GCP, Azure, Slurm|Production|
|[Toil](https://github.com/BD2KGenomics/toil)|Toil is a workflow engine entirely written in Python.|[![Build Status](https://ci.commonwl.org/job/toil-conformance/badge/icon)](http://ci.commonwl.org/job/toil-conformance/lastBuild/testReport/)|AWS, GCP, Azure, OpenStack, Grid Engine, Mesos|Production|
|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|[![Build Status](https://ci.commonwl.org/buildStatus/icon?job=rabix-conformance)](https://ci.commonwl.org/job/rabix-conformance/)|Java|alpha|
|[Apache Taverna](http://taverna.incubator.apache.org/)|Domain-independent Workflow Management System|[alpha](https://issues.apache.org/jira/browse/TAVERNA-900)|Java|Production|
|[Galaxy](https://galaxyproject.org/)|Web-based platform for data intensive biomedical research.|[alpha](https://github.com/common-workflow-language/galaxy)|Python|Production|
|[AWE](https://github.com/MG-RAST/AWE)|Workflow and resource management system for bioinformatics data analysis.|[alpha](https://github.com/wgerlach/AWE)|Go|Production|
|[Funnel](https://github.com/bmeg/funnel)|Use Google Genomics Pipeline API with CWL|alpha|GCP|alpha|
|[xenon-cwl-runner](https://github.com/NLeSC/xenon-cwl-runner)|Run CWL workflows using Xenon|alpha|[any Xenon backend](http://nlesc.github.io/Xenon/): local, ssh, SLURM, Torque, Grid Engine|Production|
|Software|Description|CWL support|Platform support|
|--------|-----------|-----------|--------|
|[cwltool](https://github.com/common-workflow-language/cwltool)|Reference implementation of CWL|[![Build Status](https://ci.commonwl.org/job/cwltool-conformance/badge/icon)](http://ci.commonwl.org/job/cwltool-conformance/lastBuild/testReport/)|Linux, OS X, local execution only|
|[Arvados](https://arvados.org)|Distributed computing platform for data analysis on massive data sets. [Using CWL on Arvados](http://doc.arvados.org/user/cwl/cwl-runner.html)|[![Build Status](https://ci.commonwl.org/job/arvados-conformance/badge/icon)](http://ci.commonwl.org/job/arvados-conformance/lastBuild/testReport/)|AWS, GCP, Azure, Slurm|
|[Toil](https://github.com/BD2KGenomics/toil)|Toil is a workflow engine entirely written in Python.|[![Build Status](https://ci.commonwl.org/job/toil-conformance/badge/icon)](http://ci.commonwl.org/job/toil-conformance/lastBuild/testReport/)|AWS, Azure, GCP, Grid Engine, LSF, Mesos, OpenStack, Slurm|
|[Rabix Bunny](https://github.com/rabix/bunny)|An open-source, Java-based implementation of Common Workflow Language with support for multiple drafts/versions. See [Rabix.io](http://rabix.io) for details.|[![Build Status](https://ci.commonwl.org/buildStatus/icon?job=rabix-conformance)](https://ci.commonwl.org/job/rabix-conformance/)|Linux, OS X, [GA4GH TES](https://github.com/ga4gh/task-execution-server) (experimental)|
|[cwl-tes](https://github.com/common-workflow-language/cwl-tes)|CWL engine backended by the [GA4GH Task Execution API](https://github.com/ga4gh/task-execution-schemas)|[![Build Status](https://travis-ci.org/common-workflow-language/cwl-tes.svg?branch=master)](https://travis-ci.org/common-workflow-language/cwl-tes)|Local, GCP, AWS, HTCondor, Grid Engine, PBS/Torque, Slurm|
|[Airflow](https://github.com/Barski-lab/incubator-airflow)|Airflow updated with CWL-runner feature (supported by BioWardrobe Team, CCHMC)|[![Build Status](https://ci.commonwl.org/buildStatus/icon?job=airflow-conformance)](https://ci.commonwl.org/job/airflow-conformance)|Linux, OS X|
|[Consonance](https://github.com/Consonance/consonance)|orchestration tool for running SeqWare workflows and CWL tools|[pending](https://ci.commonwl.org/job/rabix-conformance/)|AWS, OpenStack, Azure|
|[Apache Taverna](http://taverna.incubator.apache.org/)|Domain-independent Workflow Management System|[alpha](https://issues.apache.org/jira/browse/TAVERNA-900)|Java|
|[Galaxy](https://galaxyproject.org/)|Web-based platform for data intensive biomedical research.|[alpha](https://github.com/common-workflow-language/galaxy)|Python|
|[AWE](https://github.com/MG-RAST/AWE)|Workflow and resource management system for bioinformatics data analysis.|[alpha](https://github.com/wgerlach/AWE)|Go|
|[Xenon](http://nlesc.github.io/Xenon/)|Run CWL workflows using Xenon|[alpha](https://github.com/NLeSC/xenon-cwl-runner)|[any Xenon backend](http://nlesc.github.io/Xenon/): local, ssh, SLURM, Torque, Grid Engine|


## Repositories of CWL Tools and Workflows
Expand All @@ -71,8 +75,20 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
|[pypi2cwl](https://github.com/common-workflow-language/pypi2cwl)|Automatically run argparse2cwl on any package in PyPi|
|[cwlavro](https://github.com/common-workflow-language/cwlavro)|Java classes for loading CWL documents|
|[acd2cwl](https://github.com/common-workflow-language/acd2cwl)|CWL generator for ACD (EMBOSS) files |
|[CWLviewer](https://github.com/MarkRobbo/CWLViewer)|A web application to view and share Common Workflow Language workflows|
|[CWLviewer](https://view.commonwl.org/)|A web application to view and share Common Workflow Language workflows|
|[cwl2zshcomp](https://github.com/kloetzl/cwl2zshcomp)|generates ZSH auto completions from CWL command line tool descriptions|
|[scriptcwl](https://github.com/NLeSC/scriptcwl)|Create CWL workflows by writing a simple Python script|
|[python-cwlgen](https://github.com/common-workflow-language/python-cwlgen)|Generation of CWL programmatically from Python.|

## Projects the CWL community is participating in

|Name|Details|
|-------|-----------|
|[GA4GH Task Execution API](https://github.com/ga4gh/task-execution-schemas/)|a minimal common API for submitting a single job to a remote execution endpoint. Many contributions from CWL project participants.|
|[GA4GH Workflow Execution API](https://github.com/ga4gh/workflow-execution-schemas)|a minimal common API for submitting workflow requests to workflow execution systems in a standardized way. Many contributions from CWL project participants.|
|[Bio-compute objects](https://hive.biochemistry.gwu.edu/htscsrs?pageid=biocompute)|"a step towards evaluation and validation of bio-medical scientific computations", CWL and researchobject.org participants are cooperating with this effort|

<a name="Support"></a>
## Support, Community and Contributing

The recommended place to ask a question about all things CWL is on
Expand All @@ -87,9 +103,6 @@ join the [mailing list common-workflow-language on Google Groups](https://groups
[fork the repository](https://github.com/common-workflow-language/common-workflow-language)
and send a pull request!

Your CWL Community Engineer, Michael R. Crusoe, publishes a blog about his work
with updates at http://mrc.commonwl.org.

### Code of Conduct

The CWL Project is dedicated to providing a harassment-free experience for
Expand All @@ -114,11 +127,16 @@ Conduct](https://github.com/common-workflow-language/common-workflow-language/bl
* [Institut Pasteur](http://www.pasteur.fr)
* [Wellcome Trust Sanger Institute](https://www.sanger.ac.uk/)
* [University of California Santa Cruz](https://cbse.soe.ucsc.edu/research/bioinfo)
* [Harvard Chan School of Public Health](http://www.hsph.harvard.edu/)
* [Harvard T.H. Chan School of Public Health](http://www.hsph.harvard.edu/)
* [Cincinnati Children's Hospital Medical Center](http://www.cincinnatichildrens.org/)
* [Broad Institute](https://www.broadinstitute.org)
* [BioDatomics](http://www.biodatomics.com/)
* [Wolfson Wohl Cancer Research Centre](http://www.gla.ac.uk/researchinstitutes/cancersciences/ics/facilities/wwcrc/)
* [University of Melbourne Center for Cancer Research](https://umccr.github.io/)
* [Netherlands eScience Center](https://www.esciencecenter.nl/)
* [Texas Advanced Computing Center Life Science Computing Group](https://www.tacc.utexas.edu/life-sciences-computing) / [Agave Platform](https://agaveapi.co/)
* [CyVerse](http://www.cyverse.org/)
* [Institute for Systems Biology](https://www.systemsbiology.org/)
* [ELIXIR Europe](https://www.elixir-europe.org/)
* [BioExcel CoE](http://bioexcel.eu/)

## Individual Contributors

Expand All @@ -131,15 +149,24 @@ Conduct](https://github.com/common-workflow-language/common-workflow-language/bl
* Michael R. Crusoe <michael.crusoe@gmail.com>
* Roman Valls Guimerà <brainstorm@nopcode.org>
* Guillermo Carrasco Hernandez <guille.ch.88@gmail.com>
* Kenzo-Hugo Hillion <kehillio@pasteur.fr>
* Sinisa Ivkovic <sinisa.ivkovic@sbgenomics.com>
* Sehrish Kanwal <skanwal@student.unimelb.edu.au>
* Andrey Kartashov <Andrey.Kartashov@cchmc.org>
* John Kern <kern3020@gmail.com>
* Farah Zaib Khan <farahk@student.unimelb.edu.au>
* Dan Leehr <dan.leehr@duke.edu>
* Hervé Ménager <herve.menager@gmail.com>
* Maxim Mikheev <mikhmv@biodatomics.com>
* Michael Miller <mmiller@systemsbiology.org>
* Tim Pierce <twp@unchi.org>
* Josh Randall <joshua.randall@sanger.ac.uk>
* Mark Robinson <mark.robinson-4@student.manchester.ac.uk>
* Janko Simonović <janko.simonovic@sbgenomics.com>
* Stian Soiland-Reyes <soiland-reyes@cs.manchester.ac.uk>
* Stian Soiland-Reyes <soiland-reyes@manchester.ac.uk>
* Luka Stojanovic <luka.stojanovic@sbgenomics.com>
* Nebojša Tijanić <nebojsa.tijanic@sbgenomics.com>


The CWL Community Engineer, Michael R. Crusoe, publishes a blog about his work
with updates at http://mrc.commonwl.org.
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